NAME¶

SYNOPSIS¶

DESCRIPTION¶

Bowtie 2 version 2.3.4.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)

reference_in

comma-separated list of files with ref sequences

bt2_index_base

write bt2l data to files with this dir/basename

*** Bowtie 2 indexes work only with v2 (not v1). Likewise for v1 indexes. ***

OPTIONS¶

-c

reference sequences given on cmd line (as <reference_in>)

-a/--noauto

disable automatic -p/--bmax/--dcv memory-fitting

-p/--packed

use packed strings internally; slower, less memory

--bmax <int>

max bucket sz for blockwise suffix-array builder

--bmaxdivn <int>

max bucket sz as divisor of ref len (default: 4)

--dcv <int>

diff-cover period for blockwise (default: 1024)

--nodc

disable diff-cover (algorithm becomes quadratic)

-r/--noref

don't build .3/.4 index files

-3/--justref

just build .3/.4 index files

-o/--offrate <int>

SA is sampled every 2^<int> BWT chars (default: 5)

-t/--ftabchars <int>

# of chars consumed in initial lookup (default: 10)

--threads <int>

# of threads

--seed <int>

seed for random number generator

-q/--quiet

verbose output (for debugging)

-h/--help

print detailed description of tool and its options

--usage

print this usage message

--version

print version information and quit